University of Texas MD Anderson Cancer Center, USA
Hui Chen has completed her MD from Peking Union Medical College, PhD from Colorado State University, Postdoctoral Research Fellowship from Johns Hopkins Medical School, Residency training from Dartmouth-Hitchcock Medical Center and Clinical Fellowship training from Memorial Sloan-Kettering Cancer Center. She is an Assistant Professor in Molecular Pathology and Breast Pathology at MD Anderson Cancer Center.
Clinical laboratories are rapidly implementing next-generation sequencing (NGS) tests for mutation analysis, however there are few guidelines regarding sample quality for successful results. We aimed to establish tissue quality parameters for successful NGS in solid tumors and to improve NGS performance. Using a 50-gene hotspot mutation panel we identified the major cause for unsuccessful NGS analysis being DNA <10 ng, which was associated with extremely small and low cellularity samples. High success rates were associated with resection procedures and biopsied tumor >10 mm2. Independent factors leading to lower NGS success were cellular tumor areas and decalcification procedures. Tumor type and paraffin block age did not affect success. We optimized workflow and showed improved NGS success rates with pronounced improvement among tiny samples and cytology samples. Identifying pre-analytical tissue factors allows us to improve NGS performance and to successfully test tumors obtained from minimally invasive procedures.